Slacker
I read the app note you suggested. Here is what I am doing. I have all the pin numbers, and manual, etc. Chinese are not that great in their documentation. My board has a general clock circuit, which provides an output frequency of 50MHz that is connected to pin 10 of the Cyclone. I take this output and connect it to the PLL circuit. I connect the PLL output (c0) to the clock pin of the JK flip flop. I have connected the FF in toggle mode. I upload the circuit to the board and get a faint LED (not toggling). Maybe the PLL output frequency is too high for the FF.
Veronis